Travelex at the airport indeed has rip-off rate and ridiculous 5% comission, but I don't think there is really any need to exchange money at the airport with these thiefs. Even if you arrive without any local currency, you can:
a) withdraw cash from the ATM
b) buy public transport tickets from the Transport Company (DPP) booth (in both arrival halls, close to the exit from airside, open daily 7-22), look for illuminated red-white sign with Bus-Tram-Metro. You will need 20 CZK ticket to get from the airport. They accept plastic money, even if you pay for just two tickets (40 CZK). They also sell the the multi-day public transport passes (good for unlimited travel on any bus, metro, tram and Petrin funicular train for 24/72/168 hours) I mentioned earlier.

Good exchange office downtown is eXchange just behind the church on the Old Town Square
www.exchange.cz
or the exchange office in mezzanine of the exit from the Malostranska metro station (line A)